Contacts of the helix formed by residues 723 - 727 (chain A) in PDB entry 3BK0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 723 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ARG 4.2 10.5 - - - +
683A ASP* 3.5 20.4 - - - +
704A MET* 4.3 20.0 - - + -
721A GLN 3.4 5.8 - - - +
722A VAL* 1.4 82.7 - - + +
724A VAL* 1.3 62.2 + - - +
725A LYS 3.2 2.9 - - - -
726A TRP* 3.0 19.2 + - + -
727A THR* 2.7 29.6 + - - +
825A EDO 3.6 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A VAL* 2.8 32.1 + - + +
723A PRO* 1.3 71.6 - - - +
725A LYS* 1.3 60.7 + - + +
727A THR* 3.0 19.6 + - - +
732A LEU* 3.7 26.1 - - + +
766A ASN* 3.6 53.7 + - + +
769A THR* 4.8 0.9 - - - -
770A ARG* 3.8 12.1 - - + +
824A EDO 2.8 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PRO 3.2 1.0 - - - -
724A VAL* 1.3 75.8 - - - +
726A TRP* 1.3 79.0 + - + +
727A THR 3.5 0.4 - - - -
744A TRP* 4.8 0.7 + - - -
748A ILE* 3.8 15.4 - - - +
760A PRO* 3.5 21.9 + - + +
761A TYR* 3.0 46.4 + - + -
762A PRO* 4.6 4.4 + - - +
764A LEU 2.7 28.6 + - - -
765A SER 4.2 1.8 - - - -
766A ASN* 3.7 21.5 + - - +
769A THR* 3.4 19.7 - - + +
824A EDO 3.7 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A EDO 6.4 2.0 - - - -
645A LEU* 6.0 1.6 - - + -
683A ASP* 6.2 0.4 - - - -
684A LEU 3.4 24.9 - - - +
685A ALA* 3.4 10.3 - - + +
723A PRO* 3.0 20.1 + - + +
725A LYS* 1.3 102.2 - - + +
727A THR* 1.3 55.8 + - - +
744A TRP* 3.7 6.0 - - - -
745A SER* 2.7 39.2 + - - +
748A ILE* 3.4 27.4 - - + +
752A GLU* 2.9 38.0 + - - -
760A PRO* 3.6 28.0 - - + -
825A EDO 3.1 41.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ARG 4.7 4.7 + - - -
722A VAL* 4.3 1.2 - - - +
723A PRO* 2.7 36.5 + - - +
724A VAL 3.0 7.1 + - - -
725A LYS 3.5 0.2 - - - -
726A TRP* 1.3 80.6 - - - +
728A ALA* 1.3 63.1 + - - +
731A ALA* 3.5 25.4 - - + -
732A LEU* 3.6 25.6 - - + -
737A TYR* 3.8 16.2 + - + +
741A SER* 5.8 0.9 - - - -
744A TRP* 3.6 3.9 + - - -
745A SER* 4.5 2.2 - - - -
824A EDO 2.8 31.5 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il